The phylogenetic position of Lathyrus relative to the rest of tribe Fabeae was estimated based on sequence data from the chloroplast matK region. This study included 24 species of Lathyrus (including 19 newly sequenced). A clade containing Lathyrus, Pisum and Vavilovia is strongly supported as monophyletic. The results support the existing morphologically based hypothesis that Pisum and Vavilovia are sister genera. To study relationships within Lathyrus, accessions representing 53 of its species were sequenced for the internal transcribed spacers and 5.8S-coding region of nuclear ribosomal DNA (ITS), and the chloroplast trnL-F and trnS-G regions. Within Lathyrus, the majority of the sections are centred on the Mediterranean region, which appears to be the area of origin for the genus. Sections Orobus, Aphaca, and Pratensis form a northern Eurasian-New World clade. Within this clade, the North American and eastern Eurasian species, including both Holarctic species (L. palustris and L. japonicus), form a transberingian clade of relatively recent origin and diversification. In each phylogenetic analysis, the predominantly South American Notolathyrus group is resolved as monophyletic and unrelated to the transberingian clade. This finding refutes the traditional view that the South American species of Lathyrus are derived from the extant North American-East Asian lineage. The South American lineage may be derived from long-distance dispersals directly from Eurasia. This provides support for long-standing morphologically based hypotheses that sect. Notolathyrus is a natural grouping. A synoptic revision provides the first taxonomic treatment to cover all members of sect. Notolathyrus. The treatment recognises 26 species endemic to South America, plus a subspecies of L. pusillus extending to the southeastern USA. One species (L. bolivianus Kenicer) is described as new.